It seems like that all carriers have this problem.
At least AA didn't attempt to check-in two passengers into the same seat.
This actually happened on CX last month!
The F cabin only had 6 physical seats available, yet they were somehow able to check-in 7 passengers. 2 passengers were checked into Seat 2A on my flight!
Here is my posting in the CX forum:
http://www.flyertalk.com/forum/20812970-post1.html